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ive been having this problem for awhile in KOTOR2 since the XBOX days that just wasnt there in KOTOR1 which is with the combat. It goes a little something like this

ENEMY SPOTTED: Game Paused -> Switch to each party member and queue up their actions, Unpause -> Party members ignore first set of actions and run off to do something else, usually autoattack an enemy of *their* choosing before executing their queue -> Pause to re-issue commands and queue up actions, while switching I notice some or all of party members now have a blank action queue even though I just issued commands

It's infuriating. The system is not supposed to work this way, and in KOTOR1 when it does sometimes happen i can clear their queue completely including the "invisible" autoattack the AI queued up itself (i know this works when the selected party member "turns" or changes face) but it seems to happen all the damn time in KOTOR2 making the first round of combat an exercise in patience as the party runs off to attack entirely different enemies than what i ordered

I cant be the only one seeing this glitch
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Very interesting. I've never run across this problem, but I haven't used the pause function in years.
I play the game without pausing and fight in real-time, which is a nice added challenge and makes the combat mechanics much more enjoyable for me. The game is very easy in terms of combat difficulty, so maybe you could try that and see if it's fun for you?

Otherwise I'd guess that is just the way it's done in KotOR II, since you've encountered the problem on different platforms and I haven't seen this complaint before, though that doesn't say that much.
Maybe you could try deactivating the auto-pause at the start of a battle and pause manually yourself, see how, if at all, that changes things?